PubMed Health⌕ Search

Biomedical subjects

D J Shaffer

Publications and source records attributed to D J Shaffer.

6 recordsLinked to original sources
PubMed2004

Quantitative gene expression profiling implicates genes for susceptibility and resistance to alveolar bone loss.

Periodontal disease is one of the most prevalent chronic inflammatory diseases. There is a genetic component to susceptibility and resistance to this disease. Using a mouse model, we investigated the progression of alveolar bone loss by gene expression profiling of susceptible and resistant mouse strains (BALB/cByJ and A/J, respectively). We employed a novel and sensitive quantitative real-time PCR method to compare basal RNA transcription of a 48-gene set in the gingiva and the spleen and the subsequent changes in gene expression due to Porphyromonas gingivalis oral infection. Basal expression of interleukin-1 beta (Il1b) and tumor necrosis factor alpha (Tnf) mRNA was higher in the gingiva of the susceptible BALB/cByJ mice than in the gingiva of resistant A/J mice. Gingival Il1b gene expression increased further and Stat6 gene expression was turned on after P. gingivalis infection in BALB/cByJ mice but not in A/J mice. The basal expression of interleukin-15 (Il15) in the gingiva and the basal expression of p-selectin (Selp) in the spleen were higher in the resistant A/J mice than in the susceptible BALB/cByJ mice. In the resistant A/J mice the expression of no genes detectably changed in the gingiva after infection. These results suggest a molecular phenotype in which discrete sets of differentially expressed genes are associated with genetically determined susceptibility (Il1b, Tnf, and Stat6) or resistance (Il15 and Selp) to alveolar bone loss, providing insight into the genetic etiology of this complex disease.

Alveolar Bone Loss↗
PubMed1994

Large-scale genomic comparison using two-dimensional DNA gels.

Two-dimensional electrophoresis (2DE) of DNA fragments, in which separation occurs first by size and then by sequence variation, is a method enabling large-scale comparison of complex genomes. Combining 2DE with probing for various classes of repetitive genomic elements allows rapid and efficient comparison of thousands of fragments and millions of base-pairs of DNA distributed across most genomic regions. This approach is demonstrated here by analyzing the extent of genomic relatedness of different inbred strains of mice. Such strains are shown to differ from each other by approximately 0.2-1% of their nucleotides, above which level reproductive speciation occurs. The 2DE method of assessing the overall relationship between two genomes represents an appropriate tool for analyzing members of a single species, but is too sensitive for use in interspecies comparisons.

Animals↗
PubMed1993

Cell populations during tumorigenesis in Eu-myc transgenic mice.

Transgenic mice bearing a c-myc oncogene under control of the immunoglobulin heavy chain (Igh) enhancer (Eu-myc mice) (1, reviewed in 2) undergo a reproducible series of developmental stages and die from malignancies of the B lymphocyte lineage. To investigate the cellular events underlying tumorigenesis in this model, we quantified B lymphoid subpopulations and turnover at various stages of this process. An early stage was characterized by the presence in the blood of many large proliferating B lineage cells marked by surface antigen phenotype IgM+l-, B220low, CD5-, Mac-1low. During a prolonged intermediate 'remission' phase of different duration in each mouse, B lymphocytes in the periphery were non-proliferative, few, and of conventional phenotype (IgM+, B220+, CD5-, Mac-1-), while subsets of precursor B cells were both numerous and highly proliferative in the bone marrow. In the final stage of tumorigenesis, large proliferating cells similar in phenotype to those of the early period reappeared and increased rapidly in numbers. This B cell tumorigenic progression occurred independently of interactions with T lymphocytes. Evidence of massive cell death in the bone marrow during the intermediate phase, plus molecular characterization of the final tumors, suggested that the end of the peripheral 'remission' period and entry into the terminal stage of tumorigenesis may be due to a clone of cells acquiring the ability to circumvent normal processes of cell death and elimination that usually regulate the egress of B cells from the bone marrow to the periphery.

Age Factors↗
PubMed1991

Unexpected behavior of H2Kb mutant DNAs in denaturing gradient gel electrophoresis.

Denaturing gradient gel electrophoresis (DGGE) is based upon the different melting behaviors of DNA molecules in a chemical denaturant gradient according to their sequences. This technique has recently become a widespread tool to detect mutations. The introduction of a GC-clamp enables the detection of most single base differences between two DNA molecules. As a test system we have applied the polymerase chain reaction (PCR) in combination with DGGE to detect a number of mutations in the mouse H2Kb DNA sequence. A wide variety of spontaneous in vivo mutations of this haplotype have been reported in the C57BL/6J mouse strain and are clustered in the alpha 1 and alpha 2 domains. The combination of PCR and DGGE revealed almost all base changes present in the H2Kb mutants used. However, most of the PCR products of these mutants showed melting behavior which is not easily predicted. We suggest that in addition to current simple theory, which considers that the migration of a DNA molecule in a denaturing gradient depends primarily on its initial melting behavior, additional factors such as secondary structure in partially melted molecules may play a role and can be used to detect mutations.

Animals↗
PubMed1989

Deletions in a recombinant retrovirus genome associated with its expression in embryonal carcinoma cells.

We analyzed embryonal carcinoma cell lines infected with a recombinant Moloney murine leukemia virus. Lines that carried but did not express the neo gene retained a provirus of LTR-gag-pol-neo-LTR, where LTR is a long terminal repeat, whereas all G418-resistant lines deleted regions that included the primer binding site and the splicing donor site. This suggested the presence of multiple inhibitory elements.

Chromosome Deletion↗